Have you checked whether ${subject}_aparcAseg.mgz is well aligned with the T1 image you used to calculate ${subject}_highres2standard_warp.nii.gz? That would be where I would start. I think recon-all reorients the input T1 image as part of its processing.
Best,
Ruy
> On May 8, 2018, at 5:41 PM, Daniela Valério <[log in to unmask]> wrote:
>
> <aparcAseg_mni.pdf>